Is PTPRO p.Ser802= (c.2406T>C) pathogenic?

PTPRO p.Ser802= (c.2406T>C) is classified Benign/Likely benign in PTPRO (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-06). Rare (popmax 0.937%, afr); Associated with nephrotic syndrome, type 6.

What condition is associated with PTPRO p.Ser802= (c.2406T>C)?

PTPRO p.Ser802= (c.2406T>C) is associated with nephrotic syndrome, type 6 (ClinVar).

How common is PTPRO p.Ser802= (c.2406T>C) in the general population?

PTPRO p.Ser802= (c.2406T>C) is rare (popmax 0.937%, afr) (gnomAD).

PTPRO p.Ser802=

Q: How is Hereditary steroid-resistant nephrotic syndrome inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.2406T>C · rs61741744 · VCV1590988

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.937%, afr)

Conditions

nephrotic syndrome, type 6

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.3	GERP -4.1
Overall
CADD	0.977	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.937% African / African-American · 702/74,938 alleles

Filtering AF 0.879% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.856%

Overall 0.0483% 779/1,612,950 alleles · rare exomes 372/1,460,792 · genomes 407/152,158 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.937%	107
Remaining individualsnot grpmax-eligible	0.0672%	1,487
Middle Eastern	0.0495%	2,020
Admixed American	0.04%	2,500
European (non-Finnish)	0.000678%	147,426

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PTPRO
Protein: p.Ser802=
Coding: c.2406T>C
MANE Select: NM_030667
dbSNP: rs61741744
Type: single nucleotide variant
Location: chr12:15549195 (GRCh38)
Gene constraint: LOEUF 0.513 · pLI 0.17 (gnomAD)
Structure: AlphaFold pLDDT 77.55 · 2 PDB
Residue 802: the fibronectin type-iii 8 domain

Full PTPRO gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

nephrotic syndrome, type 6 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hereditary steroid-resistant nephrotic syndrome (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Adolescent, Adult, Antenatal, Childhood, Infancy, Neonatal

Similar variants

PTPRO p.Ala1086Val Uncertain significance ★★ ⚠ same condition
PTPRO p.Ala591Thr Uncertain significance ★★ ⚠ same condition
PTPRO p.Arg480Trp Uncertain significance ★★ same condition
PTPRO p.Arg607Gln Uncertain significance ★★ ⚠ same condition
PTPRO p.Asp162Val Uncertain significance ★★ ⚠ same condition
PTPRO p.Asp799Gly Uncertain significance ★★ ⚠ same condition
PTPRO p.Glu214Lys Uncertain significance ★★ ⚠ same condition
PTPRO p.Glu564Lys Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ptpro-p-ser802 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown